Causes and consequences of soil bacterial rarity

In the highly diverse community of soil bacteria most species occur at extremely low numbers and are consequently called the “rare biosphere”. In this thesis I studied why these species are rare whereas others are common. I found that many rare bacterial species can grow rapidly and are doing well in competition, but that rare species could be more vulnerable to predation. This might account for their rarity in soil. Still growth, competitiveness and predation resistance differed greatly between rare species. In addition, I tested if rare soil bacterial species can protect plants from insect attack by stimulating resistance mechanisms in the plant. However, there was no effect of rare bacteria on plant resistance. Rather plant response varied with different bacterial communities regardless of whether rare species were present or not. Overall, my thesis demonstrates that there are likely no general causes of bacterial rarity or general consequences for plant health.</p

Where less may be more: how the rare biosphere pulls ecosystems strings

Rare species are increasingly recognized as crucial, yet vulnerable components of Earth’s ecosystems. This is also true for microbial communities, which are typically composed of a high number of relatively rare species. Recent studies have demonstrated that rare species can have an over-proportional role in biogeochemical cycles and may be a hidden driver of microbiome function. In this review, we provide an ecological overview of the rare microbial biosphere, including causes of rarity and the impacts of rare species on ecosystem functioning. We discuss how rare species can have a preponderant role for local biodiversity and species turnover with rarity potentially bound to phylogenetically conserved features. Rare microbes may therefore be overlooked keystone species regulating the functioning of host-associated, terrestrial and aquatic environments. We conclude this review with recommendations to guide scientists interested in investigating this rapidly emerging research area

Where less may be more: how the rare biosphere pulls ecosystems strings

Rare species are increasingly recognized as crucial, yet vulnerable components of Earth’s ecosystems. This is also true for microbial communities, which are typically composed of a high number of relatively rare species. Recent studies have demonstrated that rare species can have an over-proportional role in biogeochemical cycles and may be a hidden driver of microbiome function. In this review, we provide an ecological overview of the rare microbial biosphere, including causes of rarity and the impacts of rare species on ecosystem functioning. We discuss how rare species can have a preponderant role for local biodiversity and species turnover with rarity potentially bound to phylogenetically conserved features. Rare microbes may therefore be overlooked keystone species regulating the functioning of host-associated, terrestrial and aquatic environments. We conclude this review with recommendations to guide scientists interested in investigating this rapidly emerging research area

Low abundant soil bacteria can be metabolically versatile and fast growing

Measurement data on bacterial isolates; further description see metashee

Replication Data for: Competition and predation as possible causes of bacterial rarity

This dataset contains the experimental setup and the experimental data belonging to the article "Competition and Predation as possible causes of bacterial rarity"

Report: Resistance of potato tubers against soft rot Pectobacteriaceae (SRP) : Disease resistance in potato tubers against soft rot Pectobacteriaceae

Soft rot Pectobacteriaceae (SRP) continue to cause blackleg disease and tuber soft rot during cultivation of seed tubers. Currently, there are no chemical compounds that are effective against SRP and no resistant cultivars. Past studies have indicated differences in disease incidence between tuber lots of the same cultivar. The goal of the present study was to determine if there are indeed differences in disease incidence between different lots inoculated with the currently most frequently occurring SRP species Dickeya solani and Pectobacterium brasiliense. Subsequently, we assessed if these differences were associated with differences in the tuber microbiome (bacteria and fungi) and/or the set of secondary compounds in the tuber.In two consecutive growing seasons, different lots of the cultivars Kondor and Spunta, originating from different locations, were planted in two common fields with an equal load of the two pathogens. Differences in disease incidence were assessed and in both years three lots with a high disease incidence and three lots with a low disease incidence were selected for microbiome and metabolome analysis.These lots belonged to the cultivar Kondor, as disease incidence in cultivar Spunta was generally low and no large differences could be detected. In addition, a pot experiment was conducted, in which the different lots were infected with the Rhizoctonia solani and Colletotrichum coccodes in order to determine if potential suppressiveness in the lots would also be effective against these fungal pathogens. In the second year, microbial community composition was additionally measured in the different soils that the lots originated from to compare taxa present in the tuber and in the soil. Abiotic soil parameters were measured as well to determine their potential influence on suppressiveness.In both years, differences between lots in blackleg disease incidence were found, although differences were larger in year 1 than in year 2 and disease incidence varied with location and pathogen. No differences were found in the disease incidences with R. solani and C. coccodes. Both the bacterial and the fungal community composition differed between lots with a low and a high disease incidence. In 2018, the bacterial taxa Pseudomonas sp., Curtobacterium sp., Pantoea sp. and Rhodococcus sp., as well as the fungal taxa Vishniacozyma heimaeyensis, Penicillium brevicompactum, Debaryomyceshansenii, and Rhodotorula babjevae were among the taxa that were significantly increased in tubers with a lower disease incidence, i.e. higher suppressiveness. In 2019, the bacterial taxa Staphylococcusspp., Pseudarthrobacter sp., Glutamicibacter sp., Paenarthrobacter sp., Brevibacterium sp., CandidatusUdaeobacter, and members of the Bacillacae, and the fungal taxa Fusarium oxysporum, Debaryomyceshansenii, Plectosphaerella niemejerarum, Vishniacozyma heimaeyensis, and Mycosphaerella tassianashowed most association with a low disease incidence. In soil, taxa from the genera Bacillaceae and Planoccocaceae, and the genera Candidatus Udaeobacter and Bradyrhizobium, as well as the fungi Cladosporium cladosporides, Saitozyma podzolica, Fusarium oxysporum and two species of the genus Solicoccozyma were correlated with a low disease incidence in the tubers originating from this soil. Several of these taxa have previously been described as being involved in plant growth promotion and disease suppressiveness, indicating that they might have showed antagonism against SRP. Moreover,there was a high variation between the two years and between individual lots in microbial community composition. This indicates that different taxa can increase resistance against the SRPs rather than a specific set of species. It was also found that most of the taxa that were associated with suppressivenessin the tuber were also present in the soil of origin, indicating that these taxa might have colonized the plants from the soil as endophytes. However, abundance in soil was not correlated with abundance in the tuber, meaning that also soils with a low abundance of the respective taxa can yield tubers with a high abundance and vice versa. Which factors influence recruitment and final abundance in the tubers,is poorly understood and should be subject to further investigation. In addition, no clear correlation was found between abiotic soil parameters and disease suppressiveness, indicating that suppressiveness is not dependent on soil type or mineral status within the range of soils that was tested in this study.The results of this study suggest that bacterial and fungal taxa in the soil can colonize tubers growing in the respective soil and contribute to disease suppressiveness against SRP in the following field generation. In order confirm this hypothesis, the respective taxa will have to be added to infected tubers to prove an effect in disease incidenc

Report: effects of antagonists on resistance against soft rot Pectobacteriaceae in potato

Soft rot Pectobacteriaceae (SRP), causing blackleg and soft rot in potatoes, are still a major problem in seed potato farming. Since no resistant cultivars are known yet and no chemical compounds are available with effectivity against SRP, there is increased interest in the use of biocontrol agents. In the presented study we investigated the effectivity of potential bacterial antagonists on resistance against black leg. Bacterial isolates were obtained from potato tissue or the surrounding soil as these strains are adapted to living on and in the potato ecosystem. An informed choice was made from the panel of bacterial strains, using several selection criteria: in-vitro inhibition of SRP, the ability to macerate tuber tissue, presence in high densities in tuber tissue, belonging to risk group 1, and a high taxonomic diversity. The selected antagonists were tested in a 4-year field trial. In all 4 years potato tubers of the cultivars Agria (2018), Kondor (2019) en Kondor and Mozart (2020 & 2021) were vacuum inoculated with either Pectobacterium brasiliense or Dickeya solani. Subsequently, the tubers were spray-inoculated with the selected isolates either as single strains or in combinations of three strains. In 2020 and 2021, several combinations from the previous years were used as well as new combinations. Also combinations of 2 or 5 strains were tested in addition to talc formulations of the isolates, application of the bacteria directly into the planting hole and inoculation on naturally infected tubers. Tubers were planted in the field, in 2018 and 2019 in one location and in 2020 and 2021 in two locations (sandy soil and clay soil) and scored every 2 weeks for blackleg symptoms. In 2018, plant emergence was very low and therefore only little differences could be detected between the treatments and control. In 2019, in contrast, several treatments consisting of three strain mixes were highly effective against P. brasiliense, reducing disease incidence to as low as 0%. However, when these treatments were applied again in 2020, this effect could not be replicated. In general, the effect of antagonist treatments was highly variable between the two cultivars, locations and replicates. Also in 2021, the treatment effects differed from the previous years and between locations, cultivars and replicates. Talc formulation or plant hole inoculation did not reduce disease incidence. In both 2020 and 2021, disease incidence was higher in cultivar Kondor than in cultivar Mozart and higher in sandy soil than in clay soil. In order to characterize the antagonists used in this study in more detail, the whole genomes of 78 of the used isolates were sequenced. An analysis of the presence of genes for secondary metabolite production showed that most isolates had the potential to produce antimicrobial compounds. It was also tested if the isolates were able to survive in storage for two weeks from inoculation to planting. 22 of the 25 tested strains could still be detected at relative high densities after 15 days. Moreover, plant stems from three treatments and controls were harvested at the end of the growing season in 2021 and tested for the presence of the used isolates. In only one stem of 28 stems, one of the isolates could be detected. The results indicate that the isolates had the potential to suppress SRP in potato tubers. However, it is possible that inoculation on the surface of the tuber did not lead to an effective colonization of the plants. The antagonists were exposed to the indigenous soil and tuber microflora under low temperature conditions. On the other hand, the pathogens were inoculated by vacuum inoculation and were therefore already present inside the tuber periderm in high concentrations. The effect of the antagonists may be improved if they are vacuum infiltrated into the tubers. As endophytic bacteria have been demonstrated to mostly originate from soil and colonize the plant through the roots, increase of plant resistance could be achieved through improvement of the soil microbiome and stimulating plant colonization of antagonistic bacteria. However, both soil microbiome manipulation as factors determining plant colonization are still poorly understood. More knowledge should be generated on the soil microbiome manipulation and plant colonization of biocontrol agents

Bodemgezondheidproef 2017-2020 : Langjarig onderzoek naar het effect van verschillende maatregelen en teeltsystemen op het bodemmicrobioom en ziektewering

In een lang termijn veldproef sinds 2006, zijn in 2018 10 verschillende bodemmaatregelen uitgevoerd in zowel een gangbaar als een biologisch landbouwsysteem. De maatregelen waren zwarte braak (CTR), teelt van gras/klaver (GRK), teelt van Tagetes patula (TAG), teelt van een groenbemestermengsel (MIX), compost (CMP), chitine (CHI), haarmeel (HRM), anaerobe grondontsmetting (ASD), grondontsmetting (ONT: NGO of CAL) en een combinatie van anaerobe grondontsmetting, haarmeel en compost (AHC). Vervolgens werden of verschillende tijdstippen in 2018, 2019 en 2020 een aantal microbiologische en bodembiologische parameters gemeten. In 2018 is het bodemmicrobioom geanalyseerd, i.e. de samenstelling van de bacteriële en schimmelgemeenschap in de bodem. In vergelijking met de controle was de diversiteit van beide groepen verlaagd in de diverse ontsmettingsbehandelingen. Ook verschilde de samenstelling van de microbiële gemeenschappen duidelijk tussen de ontsmettingsbehandelingen en de overige behandelingen. Wel was de DNA concentratie van zowel schimmels als bacteriën vaak hoger in met name de anaerobe grond ontsmetting (ASD) en de combi (AHC) behandeling. Het biologische en gangbare landbouwsysteem verschilden weinig van elkaar.In zowel 2018 als 2019 zijn biotoetsen uitgevoerd om de weerbaarheid van de grond tegen Rhizoctoniasolani en Pythium ultimum te meten. Voor R. solani was de ziekteincidentie in alle behandelingen hoog en er is dus nauwelijks weerbaarheid gemeten. Voor P. ultimum daarentegen was de weerbaarheid in beide jaren duidelijk hoger in de AHC behandeling dan in de andere behandelingen.In 2020 is het microbioom middels PLFA analyse onderzocht in de CTR, CMP en AHC behandelingen. Hierbij waren veel parameters, zoals de microbiële biomassa, het aantal bacteriën en schimmels en mycorrhiza verhoogd in het biologische landbouwsysteem vergeleken met het gangbare systeem. De meeste parameters waren het hoogst in de combi behandelingen, wat duidt op hogere biomassa en activiteit van het microbioom.De schimmel en bacterie biomassa werd tegelijkertijd ook met klassieke microscopische methoden in kaart gebracht. Deze toonden geen correlatie met de PLFA metingen en er waren geen significanteverschillen tussen de landbouwsystemen en behandelingen.HWC (heet-water extraheerbare koolstof) is in 2019 gemeten in alle behandelingen, met significant hogere waardes in de combi behandeling en de anaerobe grond ontsmetting. Dit komt overeen met de hogere microbiële biomassa en hogere concentratie van schimmel- en bacterie DNA. Ook de MIX, CMPen CHI behandelingen bevatten meer HWC dan de controle. In 2020 waren zowel HWC als PMN(potentieel mineraliseerbare stikstof) het hoogst in de AHC behandeling.In 2020 is in de controle, compost en combi behandelingen bodemrespiratie gemeten en het vermogen van de microbiële gemeenschap om verschillende organische stoffen te mineraliseren (i.e. Microresp).Respiratie was verhoogd in de AHC behandeling. Voor de Microresp analyse is geen duidelijk patroon van verschillen tussen de behandelingen waargenomen.Alle metingen tonen een sterk effect van de combinatie behandeling op het bodemmicrobioom, wat een van de meest ingrijpende behandelingen voorstelde. De meeste veranderingen waren positief, zoals verhoogde weerbaarheid tegen P. ultimum en een verhoogde microbiële biomassa en activiteit. Maar ook andere behandelingen, zoals compost en anaerobe grondontsmetting lieten effecten zien op het microbioom. De verschillen tussen het biologische en gangbare landbouwsysteem waren doorgaans minder groot

A low proportion of rare bacterial taxa responds to abiotic changes compared with dominant taxa

In many studies, rare bacterial taxa have been found to increase in response to environmental changes. These changes have been proposed to contribute to the insurance of ecosystem functions. However, it has not been systematically tested if rare taxa are more likely to increase in abundance than dominant taxa. Here, we study whether rare soil bacterial taxa are more likely to respond to environmental disturbances and if rare taxa are more opportunistic than dominant taxa. To test this, we applied nine different disturbance treatments to a grassland soil and observed changes in bacterial community composition over 7 days. While 12% of the dominant taxa changed in abundance, only 1% of the rare taxa showed any effect. Rare taxa increased in response to a single disturbance treatment only, while dominant taxa responded to up to five treatments. We conclude that rare taxa are not more likely to contribute to community dynamics after disturbances than dominant taxa. Nevertheless, as rare taxa outnumber abundant taxa with here 230 taxa that changed significantly, the chance is high that some of these rare taxa might act as ecologically important keystone taxa. Therefore, rare and abundant taxa might both contribute to ecosystem insurance.</p

Data for "Potato tuber origin and microbial composition determines resistance against soft rot Pectobacteriaceae"

In this study differences in disease incidence between potato seed lots inoculated with soft rot Pectobacteriaceae were assessed in two years. Subsequently the microbial communities in tubers and soils from seed lots with a low and high disease incidence were determined by amplicon sequencing